Archival chromatin characterisation in wild and laboratory mice

Raw Illumina short read sequencing data derived from chromatin conformation assays of wild Australian mouse (Mus musculus) and laboratory mouse (strain C57BL6) liver tissue. Mice were euthanised and a section of liver tissue was removed and flash frozen in liquid nitrogen and stored at -80C. Remaining tissue was then fixed for three days in 10% neutral buffered formalin prior to long-term storage in 70% ethanol.

After 2.5-5 years of storage, the fresh and formalin-preserved liver tissues underwent chromatin conformation assay treatment. The fresh tissue was processed according to the published FAIRE-Seq (Giresi et al. 2007. Genome Research, 17(6), 877-885) and MNase-Seq (Hoeijmakers and Bartfai. 2018. Methods in Molecular Biology, 1689, 83-101) protocols with some modification. The fixed liver tissue was processed with FAIRE and MNase protocols heavily adapted for heavily-fixed tissues. The input and enriched DNA fractions were library prepped using an xGen Prism DNA Library Prep Kit (Integrated DNA Technologies). The libraries were sequenced on an Illumina NovaSeq 6000 S4 flowcell with 150bp paired-end chemistry.